Bamen Bay is located at the intersection of the Wenjiao River and Wenchang River in Hainan Province (China), where mangroves have been facing a threat of water quality deterioration. Therefore, it is imperative to study the characteristics of the surface water quality on a watershed scale. Water samples were collected three times from 36 monitoring sites from 2015 to 2016. It was found that nitrate was the main inorganic nitrogen form and all the surface water types were alkaline. Meanwhile, aquaculture water had high content of nitrogen, total phosphorus, chlorophyll a (Chl.a), total organic carbon (TOC), and chemical oxygen demand (COD). Significant spatial and temporal variations were found for most parameters. However, stable isotopes of δD and δ18O indicated that river water mainly originated from atmospheric precipitation and experienced strong evaporation. The water chemistry and isotopes of the Bamen Bay, mangroves, and aquaculture water were initially affected by the mixing of fresh water and seawater, followed by evaporation. The river and reservoir water chemistry were mainly controlled by water-rock interactions and cation exchange as deduced from the ionic relationships and Gibbs plots. These interactions involved the dissolution of calcite-, bicarbonate-, carbonate-, and calcium-containing minerals. Oxidized environments (river, reservoir, and Bamen Bay) were conducive for nitrification, while anaerobic conditions (mangrove and aquaculture water) were beneficial to the reduced nitrogen forms.